Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part1_create_annotation_files.xml @ 1:a56343c142d5 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
author rnateam
date Tue, 29 Nov 2016 14:33:00 -0500
parents 93b90466d533
children 9dda0cc9ff98
comparison
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0:93b90466d533 1:a56343c142d5
1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0"> 1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.3.1">ribotaper</requirement> 3 <requirement type="package" version="1.3.1a">ribotaper</requirement>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
7 </stdio> 7 </stdio>
8 8
11 "$gtf" 11 "$gtf"
12 "$fa" 12 "$fa"
13 "$ccdsid" 13 "$ccdsid"
14 "$appris" 14 "$appris"
15 "annotation_path" 15 "annotation_path"
16
17 && 16 &&
18
19 tar 17 tar
20 "czvf" 18 "czvf"
21 "$output2" 19 "$output2"
22 "annotation_path" 20 "annotation_path"
23 21
35 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used. 33 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used.
36 "/> 34 "/>
37 </inputs> 35 </inputs>
38 <outputs> 36 <outputs>
39 <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/> 37 <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
40 <data name="output2" type="data" format="compressed_archive" label="annotation_path"/> 38 <data name="output2" type="data" format="zip" label="annotation_path"/>
41 </outputs> 39 </outputs>
42 <tests> 40 <tests>
43 <test> 41 <test>
44 <param name="gtf" value="test.gtf"/> 42 <param name="gtf" value="test.gtf"/>
45 <param name="fa" value="test.fa"/> 43 <param name="fa" value="test.fa"/>
79 exon sequences and transcript structures. 77 exon sequences and transcript structures.
80 78
81 ``Ribotaper part 1`` generates two files: 79 ``Ribotaper part 1`` generates two files:
82 80
83 - **start_stops_FAR** in BED format 81 - **start_stops_FAR** in BED format
84 - **annotation_path** in format of compressed archive 82 - **annotation_path** in format of zip
85 83
86 *Start_stops_FAR* 84 *Start_stops_FAR*
87 is used as an input for ``ribotaper part 2``. 85 is used as an input for ``ribotaper part 2``.
88 *Annotation_path* 86 *Annotation_path*
89 is used as an input for ``ribotaper part 3``. 87 is used as an input for ``ribotaper part 3``.
88
89
90 ]]></help> 90 ]]></help>
91 <citations> 91 <citations>
92 <citation type="doi">10.1038/nmeth.3688</citation> 92 <citation type="doi">10.1038/nmeth.3688</citation>
93 </citations> 93 </citations>
94 </tool> 94 </tool>